Date: Mon, 21 May 2018 20:56:18 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r470575 - in head/biology: . clustalx clustalx/files Message-ID: <201805212056.w4LKuIJn002026@repo.freebsd.org>
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Author: jwb Date: Mon May 21 20:56:17 2018 New Revision: 470575 URL: https://svnweb.freebsd.org/changeset/ports/470575 Log: biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI Approved by: jrm Differential Revision: https://reviews.freebsd.org/D15505 Added: head/biology/clustalx/ head/biology/clustalx/Makefile (contents, props changed) head/biology/clustalx/distinfo (contents, props changed) head/biology/clustalx/files/ head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h (contents, props changed) head/biology/clustalx/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon May 21 20:39:16 2018 (r470574) +++ head/biology/Makefile Mon May 21 20:56:17 2018 (r470575) @@ -20,6 +20,7 @@ SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw + SUBDIR += clustalx SUBDIR += consed SUBDIR += crux SUBDIR += ddocent Added: head/biology/clustalx/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/clustalx/Makefile Mon May 21 20:56:17 2018 (r470575) @@ -0,0 +1,36 @@ +# $FreeBSD$ + +PORTNAME= clustalx +DISTVERSION= 2.1 +CATEGORIES= biology +MASTER_SITES= http://www.clustal.org/download/current/ \ + ftp://ftp.ebi.ac.uk/pub/software/clustalw2/${DISTVERSION}/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Multiple alignment of nucleic acid and protein sequences with GUI + +LICENSE= LGPL3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= qmake +USE_QT4= corelib gui moc qmake_build xml + +PLIST_FILES= bin/clustalx \ + ${DATADIR}/colprot.xml \ + ${DATADIR}/coldna.xml \ + ${DATADIR}/colprint.xml \ + ${DATADIR}/clustalx.hlp + +post-patch: + @${REINPLACE_CMD} -e 's|col.*.xml|${DATADIR}/&|' \ + ${WRKSRC}/ClustalQtParams.h + @${REINPLACE_CMD} -e 's|clustalx.hlp|${DATADIR}/&|' \ + ${WRKSRC}/HelpDisplayWidget.cpp + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/clustalx ${STAGEDIR}${PREFIX}/bin + @${MKDIR} ${STAGEDIR}${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/col*.xml ${WRKSRC}/clustalx.hlp \ + ${STAGEDIR}${DATADIR} + +.include <bsd.port.mk> Added: head/biology/clustalx/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/clustalx/distinfo Mon May 21 20:56:17 2018 (r470575) @@ -0,0 +1,3 @@ +TIMESTAMP = 1526839706 +SHA256 (clustalx-2.1.tar.gz) = e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05 +SIZE (clustalx-2.1.tar.gz) = 341649 Added: head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h Mon May 21 20:56:17 2018 (r470575) @@ -0,0 +1,11 @@ +--- clustalW/general/VectorOutOfRange.h.orig 2018-05-20 18:08:08 UTC ++++ clustalW/general/VectorOutOfRange.h +@@ -5,6 +5,8 @@ + */ + #include <stdexcept> + #include <exception> ++#include <string> ++ + namespace clustalw + { + Added: head/biology/clustalx/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/clustalx/pkg-descr Mon May 21 20:56:17 2018 (r470575) @@ -0,0 +1,8 @@ +ClustalX is the graphical version of Clustal, a general purpose multiple +sequence alignment program for DNA or proteins. It produces biologically +meaningful multiple sequence alignments of divergent sequences. It calculates +the best match for the selected sequences, and lines them up so that the +identities, similarities and differences can be seen. Evolutionary +relationships can be seen via viewing Cladograms or Phylograms. + +WWW: http://www.clustal.org/
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